* minor model training logging improvement

* make port configurable

* added autocut-start-cloud

Bumps [nltk](https://github.com/nltk/nltk) from 3.4.1 to 3.4.3.
- [Release notes](https://github.com/nltk/nltk/releases)
- [Changelog](https://github.com/nltk/nltk/blob/develop/ChangeLog)
- [Commits](https://github.com/nltk/nltk/compare/3.4.1...3.4.3

)

Signed-off-by: dependabot-preview[bot] <support@dependabot.com>

Bumps [lxml](https://github.com/lxml/lxml) from 4.3.3 to 4.3.4.
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](https://github.com/lxml/lxml/compare/lxml-4.3.3...lxml-4.3.4

)

Signed-off-by: dependabot-preview[bot] <support@dependabot.com>

* move checkout and move to master into containers node

* use elifePipeline

* push unstable image

Bumps [numpy](https://www.numpy.org) from 1.16.2 to 1.16.4.

Bumps [apache-beam](https://github.com/apache/beam) from 2.12.0 to 2.13.0.
- [Release notes](https://github.com/apache/beam/releases)
- [Commits](https://github.com/apache/beam/compare/v2.12.0...v2.13.0)

Bumps [pytest](https://github.com/pytest-dev/pytest) from 4.6.1 to 4.6.2.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/4.6.1...4.6.2)

* added dev-venv target

* added subextract model

* added nltk dependency

* flake8 ignore line break before binary operator

* moved dev dependencies up

* added nltk punkt download

* added nltk download to dev-venv; pytest and pytest-not-slow target

* added subextract training pipeline

* added optional xpath namespaces

* log failed xml file

* use recover parser option

* added subextract app

* start subextract server

* renamed to autocut

* declare slow and very_slow pytest markers

* make autocut main test as slow

* fixed post data

* updated README

* also build non-dev image as part of ci

* added pytest.ini to dev image

Bumps [pytest](https://github.com/pytest-dev/pytest) from 4.5.0 to 4.6.1.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/4.5.0...4.6.1)

Bumps [cython](https://github.com/cython/cython) from 0.29.9 to 0.29.10.
- [Release notes](https://github.com/cython/cython/releases)
- [Changelog](https://github.com/cython/cython/blob/master/CHANGES.rst)
- [Commits](https://github.com/cython/cython/compare/0.29.9...0.29.10)

* added Makefile; optionally install dev requirements

* added ci-build-and-test

* use ci-build-and-test

* don't install dev dependencies as part of project_tests

* renamed to dev

* use PROJECT_FOLDER for consistency with other projects

* change order of tests run

Bumps [requests](https://github.com/requests/requests) from 2.21.0 to 2.22.0.
- [Release notes](https://github.com/requests/requests/releases)
- [Changelog](https://github.com/kennethreitz/requests/blob/master/HISTORY.md)
- [Commits](https://github.com/requests/requests/compare/v2.21.0...v2.22.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [pytest](https://github.com/pytest-dev/pytest) from 4.4.1 to 4.5.0.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/4.4.1...4.5.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [apache-beam](https://github.com/apache/beam) from 2.11.0 to 2.12.0.
- [Release notes](https://github.com/apache/beam/releases)
- [Commits](https://github.com/apache/beam/compare/v2.11.0...v2.12.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.31.1 to 4.32.1.
- [Release notes](https://github.com/tqdm/tqdm/releases)
- [Commits](https://github.com/tqdm/tqdm/compare/v4.31.1...v4.32.1

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [sciencebeam-utils](https://github.com/elifesciences/sciencebeam-utils) from 0.0.1 to 0.0.5.
- [Release notes](https://github.com/elifesciences/sciencebeam-utils/releases)
- [Commits](https://github.com/elifesciences/sciencebeam-utils/compare/v0.0.1...v0.0.5

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [cython](https://github.com/cython/cython) from 0.29.7 to 0.29.9.
- [Release notes](https://github.com/cython/cython/releases)
- [Changelog](https://github.com/cython/cython/blob/master/CHANGES.rst)
- [Commits](https://github.com/cython/cython/compare/0.29.7...0.29.9)

* Bump tensorflow from 1.12.0 to 1.13.1

Bumps [tensorflow](https://github.com/tensorflow/tensorflow) from 1.12.0 to 1.13.1.
- [Release notes](https://github.com/tensorflow/tensorflow/releases)
- [Changelog](https://github.com/tensorflow/tensorflow/blob/master/RELEASE.md)
- [Commits](https://github.com/tensorflow/tensorflow/compare/v1.12.0...v1.13.1

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

* disables two pylint warnings after security upgrade to tensorflow 1.13.1

* dropped 'futures' version requirement for python3

Bumps [pytest](https://github.com/pytest-dev/pytest) from 4.4.0 to 4.4.1.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/4.4.0...4.4.1

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [cython](https://github.com/cython/cython) from 0.29.6 to 0.29.7.
- [Release notes](https://github.com/cython/cython/releases)
- [Changelog](https://github.com/cython/cython/blob/master/CHANGES.rst)
- [Commits](https://github.com/cython/cython/compare/0.29.6...0.29.7

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

* added root user check in setup.py

* also check SCIENCEBEAM_GYM_NO_APT

Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 2.2.3 to 2.2.4.
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](https://github.com/matplotlib/matplotlib/compare/v2.2.3...v2.2.4

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.30.0 to 4.31.1.
- [Release notes](https://github.com/tqdm/tqdm/releases)
- [Commits](https://github.com/tqdm/tqdm/compare/v4.30.0...v4.31.1

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [numpy](https://www.numpy.org

) from 1.16.1 to 1.16.2.

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [lxml](https://github.com/lxml/lxml) from 4.3.2 to 4.3.3.
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](https://github.com/lxml/lxml/compare/lxml-4.3.2...lxml-4.3.3

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [pytest](https://github.com/pytest-dev/pytest) from 4.3.0 to 4.4.0.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/4.3.0...4.4.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [tensorflow-transform](https://github.com/tensorflow/transform) from 0.11.0 to 0.13.0.
- [Release notes](https://github.com/tensorflow/transform/releases)
- [Changelog](https://github.com/tensorflow/transform/blob/master/RELEASE.md)
- [Commits](https://github.com/tensorflow/transform/compare/v0.11.0...v0.13.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [apache-beam](https://github.com/apache/beam) from 2.9.0 to 2.11.0.
- [Release notes](https://github.com/apache/beam/releases)
- [Commits](https://github.com/apache/beam/compare/v2.9.0...v2.11.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [lxml](https://github.com/lxml/lxml) from 4.3.1 to 4.3.2.
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](https://github.com/lxml/lxml/compare/lxml-4.3.1...lxml-4.3.2

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [cython](https://github.com/cython/cython) from 0.29.5 to 0.29.6.
- [Release notes](https://github.com/cython/cython/releases)
- [Changelog](https://github.com/cython/cython/blob/master/CHANGES.rst)
- [Commits](https://github.com/cython/cython/compare/0.29.5...0.29.6

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [flake8](https://gitlab.com/pycqa/flake8) from 3.7.6 to 3.7.7.
- [Release notes](https://gitlab.com/pycqa/flake8/tags)
- [Commits](https://gitlab.com/pycqa/flake8/compare/3.7.6...3.7.7

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [flake8](https://gitlab.com/pycqa/flake8) from 3.7.5 to 3.7.6.
- [Release notes](https://gitlab.com/pycqa/flake8/tags)
- [Commits](https://gitlab.com/pycqa/flake8/compare/3.7.5...3.7.6

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [pytest](https://github.com/pytest-dev/pytest) from 4.2.1 to 4.3.0.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/4.2.1...4.3.0

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [pytest](https://github.com/pytest-dev/pytest) from 4.2.0 to 4.2.1.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/4.2.0...4.2.1

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [cython](https://github.com/cython/cython) from 0.29.4 to 0.29.5.
- [Release notes](https://github.com/cython/cython/releases)
- [Changelog](https://github.com/cython/cython/blob/master/CHANGES.rst)
- [Commits](https://github.com/cython/cython/compare/0.29.4...0.29.5

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [lxml](https://github.com/lxml/lxml) from 4.3.0 to 4.3.1.
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](https://github.com/lxml/lxml/compare/lxml-4.3.0...lxml-4.3.1

)

Signed-off-by: dependabot[bot] <support@dependabot.com>

Bumps [flake8](https://gitlab.com/pycqa/flake8) from 3.7.4 to 3.7.5.
- [Release notes](https://gitlab.com/pycqa/flake8/tags)
- [Commits](https://gitlab.com/pycqa/flake8/compare/3.7.4...3.7.5

)

Signed-off-by: dependabot[bot] <support@dependabot.com>